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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAATACAGAGAATACTTGGAACATATTTTGGAATATCTGACATCATTTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtcttattttaccattttctatattaatgtccatttgtgttccacatgtttatgtgattatgtagaggatcatactttgctttgtattttttaact...

Basic information

species Zea mays
transcript GRMZM2G178227_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178227_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g50850.2 (Oryza sativa), 5'ss of exon 6
AAAATACAGAGAATACTTGGAACATATTTTGGAATATCTGACATCATTTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtcttattttaccattttctatattaatgtccatttgtgttccacatgtttatgtgattatgtagaggatcatactttgctttgtattttttaact--
  |||||||||||||| |||| ||||||||||| |||||||||||||||||||||| |||||| ||||||||||||||||| |||||||||  ||||||   | ||   ||   | |||| || || |    ||| ||| ||     | ||    |  | |  |  | |     ||  ||  || |||||   |  |  
GCAATACAGAGAATACCTGGAGCATATTTTGGAGTATCTGACATCATTTCTGTATCACACAGAACCATTGCAAGACATTGAGAAGATTTTTGCAAAGgttcctattccctt--tactttcaattttgagcatcatatgttttagttttattatcctactgacttctatgtaatgacaatgtattctatttaagagttca
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|8367537|gb|BE050482.1|BE050482
EST:     TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGANNNNNNNAAAG                         CTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
genomic: TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
EST: gi|60393978|gb|DN226848.1|DN226848
EST:     TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGANNNNNNNAAAG                         CTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
genomic: TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
EST: gi|76290494|gb|DV030062.1|DV030062
EST:     TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGANNNNNNNAAAG                         CTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
genomic: TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
EST: gi|31353537|gb|CD437894.1|CD437894
EST:     TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGANNNNNNNAAAG                         CTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
genomic: TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
EST: gi|20802738|gb|BQ293788.1|BQ293788
EST:     TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGANNNNNNNAAAG                         CTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
genomic: TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
EST: gi|8367536|gb|BE050481.1|BE050481
EST:     TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGANNNNNNNAAAG                         CTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
genomic: TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
EST: gi|31358406|gb|CD442763.1|CD442763
EST:     TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGANNNNNNNAAAG                         CTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
genomic: TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
EST: gi|26456323|gb|CA827906.1|CA827906
EST:     TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGANNNNNNNAAAG                         CTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG
genomic: TTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 385

AAAATACAGAGAATACTTGGAACATATTTTGGAATATCTGACATCATTTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGGGGGAATAAAGGGACAGAAAAAGAGTCTGAAATAGATCTCGATTACTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 305

AAAATACAGAGAATACTTGGAACATATTTTGGAATATCTGACATCATTTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGGGGGAATAAAGGGACAGAAAAAGAGTCTGAAATAGATCTCGATTACTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 302

AAAATACAGAGAATACTTGGAACATATTTTGGAATATCTGACATCATTTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGGGGGAATAAAGGGACAGAAAAAGAGTCTGAAATAGATCTCGATTACTACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 154

AAAATACAGAGAATACTTGGAACATATTTTGGAATATCTGACATCATTTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtctta ... attggtacagCTGGAGAGTGAATTCGAGGAACAATGGGCCAATGAAGGAATACTTGGATGGGGGAATAAAGGGACAGAAAAAGAGTCTGAAATAGATCTCGATTACTACA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAATACAGAGAATACTTGGAACATATTTTGGAATATCTGACATCATTTCTGTATCGCACAGAGCCATTGCAAGACATTGATAAGATTTTTTTAAAGgtcagtcttattttaccattttctatattaatgtccatttgtgttccacatgtttatgtgattatgtagaggatcatactttgctttgtattttttaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA